Regarding the first part, it's not so much specific to whales, but just that even for a non-whale, you could eventually claw your way to the top.
It could just be via luck, or (far more likely) through extended periods of careful spending and use of UoCs.

But yes, I also dislike start of turn effects in general. As you say, it adds up, to the point that I'll remove units with excessive start-of-turn buffs from grinding parties.

Upgrade Package has one start-of-turn effect with an irreplaceable property though -- the MP restoration at the start of turn is the only hard counter for super-strong MP drains.
Regular MP regen occurs at the end of a turn, so it is useless in that regard.
To get past it now you would need a unit who could restore MP without using any MP (eg. certain unit's LBs, or limit-gauge consuming abilities).
Situationally, that would be more than worth the slight delay, though it isn't useful in most grindy content (unless we get like a multi-Hasiko wave battle or some shit like that).